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Param validation #183

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Param validation #183

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Mia0509
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@Mia0509 Mia0509 commented Nov 8, 2023

PR checklist

This PR fix the point 1 of issue #62, where providing a single number for --bin_size in the command line make the pipeline fail (due to parameter validation expecting a String and a single number is considered as an Integer (even when adding quote in command line, Unix strip those automatically)).

The fix is applied for the other parameters with same validation error (res_dist_decay, res_tads and res_compartments).

Here's what was done:

  • Add of a function to replace manually the parameter validation from the nextflow_schema.json. It happens in WorkflowHic.groovy with the digestion parameters check as the function checkParamIntList.
  • In the same file, add of a function to don't apply the .splitCsv().flatten() on the parameter if it's an Integer, which gives a error otherwise. This is called in hic.nf when combining all maps resolution.
  • Those 4 parameters are added to schema_ignore_param in all the configs file, so the original validation don't throw an error and the parameters are still referred in the schema.

Hope this little fix can be useful!

@maxulysse
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I think we should merge #177 first and maybe have a look on how to deal with this params validation with the nf-validation plugin.

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github-actions bot commented Nov 8, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit ce2cd3a

+| ✅ 148 tests passed       |+
!| ❗   1 tests had warnings |!
-| ❌  10 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • files_unchanged - CODE_OF_CONDUCT.md does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/nf-core-hic_logo_light.png does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-08 15:31:15

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@Mia0509 @maxulysse